+Open data
-Basic information
Entry | Database: PDB / ID: 7doo | ||||||
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Title | Crystal Structure of PenA beta-Lactamase-Avibactam Complex | ||||||
Components | Beta-lactamase | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information beta-lactam antibiotic catabolic process / beta-lactamase activity / beta-lactamase / response to antibiotic Similarity search - Function | ||||||
Biological species | Burkholderia multivorans ATCC 17616 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å | ||||||
Authors | Nukaga, M. / Papp-Wallace, K.M. / Bonomo, R.A. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Acs Infect Dis. / Year: 2017 Title: Overcoming an Extremely Drug Resistant (XDR) Pathogen: Avibactam Restores Susceptibility to Ceftazidime for Burkholderia cepacia Complex Isolates from Cystic Fibrosis Patients. Authors: Papp-Wallace, K.M. / Becka, S.A. / Zeiser, E.T. / Ohuchi, N. / Mojica, M.F. / Gatta, J.A. / Falleni, M. / Tosi, D. / Borghi, E. / Winkler, M.L. / Wilson, B.M. / LiPuma, J.J. / Nukaga, M. / Bonomo, R.A. #1: Journal: ACS Infect Dis / Year: 2017 Title: Overcoming an Extremely Drug Resistant (XDR) Pathogen: Avibactam Restores Susceptibility to Ceftazidime for Burkholderia cepacia Complex Isolates from Cystic Fibrosis Patients. Authors: Papp-Wallace, K.M. / Becka, S.A. / Zeiser, E.T. / Ohuchi, N. / Mojica, M.F. / Gatta, J.A. / Falleni, M. / Tosi, D. / Borghi, E. / Winkler, M.L. / Wilson, B.M. / LiPuma, J.J. / Nukaga, M. / Bonomo, R.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7doo.cif.gz | 174 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7doo.ent.gz | 136.2 KB | Display | PDB format |
PDBx/mmJSON format | 7doo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/do/7doo ftp://data.pdbj.org/pub/pdb/validation_reports/do/7doo | HTTPS FTP |
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-Related structure data
Related structure data | 3w4qS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 29452.244 Da / Num. of mol.: 3 / Fragment: Beta-lactamase, UNP residues 28-302 Source method: isolated from a genetically manipulated source Details: cleavable N-terminal GST tag Source: (gene. exp.) Burkholderia multivorans ATCC 17616 (bacteria) Strain: ATCC 17616 / Gene: ampC, BMULJ_04828 / Plasmid: PET48B / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KN52, beta-lactamase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.4 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 20% PEG8000, 0.1M HEPES, 0.2M Sodium Chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 89867 / Num. obs: 89867 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.23 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.38 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.701 / Mean I/σ(I) obs: 2.28 / Num. unique obs: 4422 / Rsym value: 0.701 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3w4q Resolution: 1.6→20 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 20.22 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.6182 Å
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